Package picard.sam.markduplicates
Class CollectDuplicateMetrics
java.lang.Object
picard.cmdline.CommandLineProgram
picard.analysis.SinglePassSamProgram
picard.sam.markduplicates.CollectDuplicateMetrics
Collect DuplicateMark'ing metrics from an input file that was already Duplicate-Marked.
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Field Summary
FieldsFields inherited from class picard.analysis.SinglePassSamProgram
ASSUME_SORTED, INPUT, output, OUTPUT, STOP_AFTERFields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected voidacceptRead(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref) Should be implemented by subclasses to accept SAMRecords one at a time.protected voidfinish()Should be implemented by subclasses to do one-time finalization work.protected OutputArgumentCollectionprotected booleanprotected voidShould be implemented by subclasses to do one-time initialization work.protected booleanCan be overridden and set to false if the section of unmapped reads at the end of the file isn't needed.Methods inherited from class picard.analysis.SinglePassSamProgram
doWork, makeItSo, setReferenceSequenceMethods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser
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Field Details
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METRICS_FILE
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Constructor Details
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CollectDuplicateMetrics
public CollectDuplicateMetrics()
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Method Details
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getOutputArgumentCollection
- Overrides:
getOutputArgumentCollectionin classSinglePassSamProgram
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requiresReference
protected boolean requiresReference()- Overrides:
requiresReferencein classCommandLineProgram
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usesNoRefReads
protected boolean usesNoRefReads()Description copied from class:SinglePassSamProgramCan be overridden and set to false if the section of unmapped reads at the end of the file isn't needed.- Overrides:
usesNoRefReadsin classSinglePassSamProgram
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setup
Description copied from class:SinglePassSamProgramShould be implemented by subclasses to do one-time initialization work.- Specified by:
setupin classSinglePassSamProgram
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acceptRead
protected void acceptRead(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref) Description copied from class:SinglePassSamProgramShould be implemented by subclasses to accept SAMRecords one at a time. If the read has a reference sequence and a reference sequence file was supplied to the program it will be passed as 'ref'. Otherwise 'ref' may be null.- Specified by:
acceptReadin classSinglePassSamProgram
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finish
protected void finish()Description copied from class:SinglePassSamProgramShould be implemented by subclasses to do one-time finalization work.- Specified by:
finishin classSinglePassSamProgram
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